Esther Rheinbay (http://csb.mgh.harvard.edu/bradley_bernstein) talks about the current challenges of visualizing rapidly expanding epigenetic data and showcases some of the different tools which are available to researchers as part of the Integrative Genome Viewer...

Keywords: Genome, Molecular

Resource type: Video

Visualization of Epigenetic Datahttps://bivi.co/presentation/visualization-epigenetic-datahttps://tess.elixir-europe.org/materials/visualization-of-epigenetic-dataEsther Rheinbay (http://csb.mgh.harvard.edu/bradley_bernstein) talks about the current challenges of visualizing rapidly expanding epigenetic data and showcases some of the different tools which are available to researchers as part of the Integrative Genome Viewer (http://www.broadinstitute.org/igv/), the Roadmap Epigenomics Project (http://www.roadmapepigenomics.org/) and ECODE project (http://genome.ucsc.edu/encode/). This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Genome, Molecular2017-01-31

Ting Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in...

Keywords: Genome, Molecular

Resource type: Slideshow, Video

Epigenome Browserhttps://bivi.co/presentation/epigenome-browserhttps://tess.elixir-europe.org/materials/epigenome-browserTing Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in multiple tracks, upload their own data as well as explore long-range interactions. He also highlights the need for the genome browsers to act as community resources and bioinformatics engines with the ability to analyse the mined data. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Dr. Ting WangGenome, Molecular2017-01-31

Jim Zheng (http://www.uthouston.edu/sbmi/faculty-and-staff/jim-zheng.htm) talks about the importance of understanding the 3D structure of genome and gives an introduction into Genome3D framework (http://www.genome3d.org/) which allows integration of multi-scale structural and genomic data within...

Keywords: Genome, Molecular

Resource type: Video

Browsing 3D Genomeshttps://bivi.co/presentation/browsing-3d-genomeshttps://tess.elixir-europe.org/materials/browsing-3d-genomesJim Zheng (http://www.uthouston.edu/sbmi/faculty-and-staff/jim-zheng.htm) talks about the importance of understanding the 3D structure of genome and gives an introduction into Genome3D framework (http://www.genome3d.org/) which allows integration of multi-scale structural and genomic data within 3D. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Genome, Molecular2017-01-31

Paul Gardner (http://www.biol.canterbury.ac.nz/people/gardner.shtml) talks about the challenges of visualization of RNA Structures and Alignments in the context of Rfam database (http://rfam.sanger.ac.uk/), a collection of non-coding RNAs, structured cis-regulatory elements and self-splicing...

Keywords: Genome, Molecular

Resource type: Video

Visualizing RNA Structures and Alignmentshttps://bivi.co/presentation/visualizing-rna-structures-and-alignmentshttps://tess.elixir-europe.org/materials/visualizing-rna-structures-and-alignmentsPaul Gardner (http://www.biol.canterbury.ac.nz/people/gardner.shtml) talks about the challenges of visualization of RNA Structures and Alignments in the context of Rfam database (http://rfam.sanger.ac.uk/), a collection of non-coding RNAs, structured cis-regulatory elements and self-splicing RNAs. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Genome, Molecular2017-01-31

Gisela Storz (http://irp.nih.gov/pi/gisela-storz) talks about the reliability and co-relation of anti-sense RNA sequence data. Comparison of RNA seq data across different experiments and from various sources reveals some discrepancies and lack of overlap. While the majority of RNA seq data is...

Keywords: Genome, Molecular

Resource type: Video

Non-coding RNAhttps://bivi.co/presentation/non-coding-rnahttps://tess.elixir-europe.org/materials/non-coding-rnaGisela Storz (http://irp.nih.gov/pi/gisela-storz) talks about the reliability and co-relation of anti-sense RNA sequence data. Comparison of RNA seq data across different experiments and from various sources reveals some discrepancies and lack of overlap. While the majority of RNA seq data is robust and reliable, low abundance transcripts can be difficult to account for and the variations in experimental as well as computational conditions can lead to vastly different data.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Genome, Molecular2017-01-31

Sean O'Donoghue (http://odonoghuelab.org) talks about molecular spatial data and the emerging issue of sequence-structure gap mainly due to experimental difficulties in obtaining reliable (or any) structure information for a given protein. In his talk, he also gives a brief demonstration of...

Keywords: Molecular

Resource type: Video

Visualizing Protein Structures and Featureshttps://bivi.co/presentation/visualizing-protein-structures-and-featureshttps://tess.elixir-europe.org/materials/visualizing-protein-structures-and-featuresSean O'Donoghue (http://odonoghuelab.org) talks about molecular spatial data and the emerging issue of sequence-structure gap mainly due to experimental difficulties in obtaining reliable (or any) structure information for a given protein. In his talk, he also gives a brief demonstration of Aquaria (http://aquaria.ws), a web-based 3D molecular structure visualization tool that combines data from various databases and allows investigators to easily view and explore proteins and protein-protein interactions.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Dr. Sean I O’DonoghueMolecular2017-01-31

Thomas Ferrin (http://www.cgl.ucsf.edu/home/tef/) talks about visualization tools for interactive modeling of biological structures with an emphasis on Chimera (http://www.cgl.ucsf.edu/chimera/), an extensible molecular modeling software.This talk was presented at VIZBI 2013, an international...

Keywords: Molecular

Resource type: Video

Comparison and assemblieshttps://bivi.co/presentation/comparison-and-assemblieshttps://tess.elixir-europe.org/materials/comparison-and-assembliesThomas Ferrin (http://www.cgl.ucsf.edu/home/tef/) talks about visualization tools for interactive modeling of biological structures with an emphasis on Chimera (http://www.cgl.ucsf.edu/chimera/), an extensible molecular modeling software.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Prof. Thomas FerrinMolecular2017-01-31

Ian Sillitoe (http://orengogroup.info/) talks about the protein structure classification with particular emphasis on superfamily-centric taxonomy which is used in the CATH (http://www.cathdb.info/) database.This video was filmed and distributed with permission under a Creative Commons...

Keywords: Molecular

Resource type: Video

Evolution of Protein Structure and Functionhttps://bivi.co/presentation/evolution-protein-structure-and-functionhttps://tess.elixir-europe.org/materials/evolution-of-protein-structure-and-functionIan Sillitoe (http://orengogroup.info/) talks about the protein structure classification with particular emphasis on superfamily-centric taxonomy which is used in the CATH (http://www.cathdb.info/) database.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Molecular2017-01-31

Martin Miller talks about visualization of proteome data with particular emphasis on modeling phosphorylation sites. He gives a brief introduction into different methods for the analysis of the single cell proteome from antibody-based methods to mass spectrometry and fluorescence tagging. With...

Keywords: Molecular

Resource type: Video

Data visualization in proteomicshttps://bivi.co/presentation/data-visualization-proteomicshttps://tess.elixir-europe.org/materials/data-visualization-in-proteomicsMartin Miller talks about visualization of proteome data with particular emphasis on modeling phosphorylation sites. He gives a brief introduction into different methods for the analysis of the single cell proteome from antibody-based methods to mass spectrometry and fluorescence tagging. With the onset of targeted and shot-gun mass spectrometry, there is an increasing amount of proteomics data which will need to be classified, integrated and available for analysis in a meaningful and accessible manner.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.Molecular2017-01-31

In this presentation David Goodsell reveals the beauty of science through his scientific and artistic endeavors. He explores the visual techniques which have been used to communicate the detail of the molecular biology world to different audiences.David Goodsell (http://bit.ly/DGoodsell) is an...

Keywords: Molecular, Communication

Resource type: Video

Making Science Beautifulhttps://bivi.co/presentation/making-science-beautifulhttps://tess.elixir-europe.org/materials/making-science-beautifulIn this presentation David Goodsell reveals the beauty of science through his scientific and artistic endeavors. He explores the visual techniques which have been used to communicate the detail of the molecular biology world to different audiences.David Goodsell (http://bit.ly/DGoodsell) is an Associate Professor of Molecular Biology at the Scripps Institute, California Campus.
Created at: VIZBI 2014.Molecular, Communication2017-01-31

Dr Nils Gehlenborg gives his keynote at 1st BiVi in 2014. The rapid proliferation of high quality, low cost genome-wide measurement technologies such as whole-genome and transcriptome sequencing, as well as advances in epigenomics and proteomics, are enabling researchers to perform studies that...

Keywords: Genome, Molecular

Resource type: Video

Visualization Approaches for Biomedical Omics Data: Putting It All Togetherhttps://bivi.co/presentation/visualization-approaches-biomedical-omics-data-putting-it-all-togetherhttps://tess.elixir-europe.org/materials/visualization-approaches-for-biomedical-omics-data-putting-it-all-togetherDr Nils Gehlenborg gives his keynote at 1st BiVi in 2014. The rapid proliferation of high quality, low cost genome-wide measurement technologies such as whole-genome and transcriptome sequencing, as well as advances in epigenomics and proteomics, are enabling researchers to perform studies that generate heterogeneous datasets for cohorts of thousands of individuals. A common feature of these studies is that a collection of genome-wide, molecular data types and phenotypic or clinical characterizations are available for each individual. These data can be used to identify the molecular basis of diseases and to characterize and describe the variations that are relevant for improved diagnosis, prognosis and targeted treatment of patients. An example for a study in which this approach has been successfully applied is The Cancer Genome Atlas project (http://cancergenome.nih.gov).In this talk Dr Gehlenborg discusses how visualization approaches can be applied to enable exploration and support analysis of data generated by such studies. Specifically, he reviews techniques and tools for visual exploration of individual omics data types, their ability to scale to large numbers of individuals or samples, and emerging techniques that integrate multiple omics data types for interactive visual analysis. He also examines technical and legal challenges that developers of such visualization tools are facing. To conclude the talk, he outlines research opportunities for the biological data visualization community that address major challenges in this domain.
Created at: 1st BiVi Annual Meeting.Dr. Nils GehlenborgGenome, Molecular2017-02-02

Dr Stephen Laycock describes using InteractinHaptiMOL to interact with large biomolecules using haptic feedback at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Slideshow

Interacting with large biomolecules using haptic feedbackhttps://bivi.co/presentation/interacting-large-biomolecules-using-haptic-feedbackhttps://tess.elixir-europe.org/materials/interacting-with-large-biomolecules-using-haptic-feedbackDr Stephen Laycock describes using InteractinHaptiMOL to interact with large biomolecules using haptic feedback at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.Dr. Stephen David LaycockMolecular2017-02-03

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on...

Keywords: Molecular, Information visualisation

Resource type: Slideshow

Visualization of Biomolecular Structures: State of the Arthttps://bivi.co/presentation/visualization-biomolecular-structures-state-arthttps://tess.elixir-europe.org/materials/visualization-of-biomolecular-structures-state-of-the-artStructural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling-Curve, surface, solid, and object representations
Created at: EuroVis 2015.Barbara KozlikovaMichael KroneMolecular, Information visualisation2017-02-28

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT &amp; Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Art and Science: A partnership catalyzing discovery in biomedicinehttps://bivi.co/presentation/art-and-science-partnership-catalyzing-discovery-biomedicinehttps://tess.elixir-europe.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicineA 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT &amp; Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT &amp; Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science.
Created at: 3rd BiVi Annual Meeting (2017).Bang WongPhylogeneticsPathway or networkAnatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation2017-05-12

In this talk Michael Sternberg of Imperial reports how their research on protein modelling has led to the development of computer games with a role in scientific education. At Imperial, Chris Reynolds has developed a web-based molecular graphics resource EzMol which is a simple-to-use display of...

Keywords: Molecular

Resource type: Video

EzMol and BioBlox: From Resources for Protein Modelling to Educational Computer Gameshttps://bivi.co/presentation/ezmol-and-bioblox-resources-protein-modelling-educational-computer-gameshttps://tess.elixir-europe.org/materials/ezmol-and-bioblox-from-resources-for-protein-modelling-to-educational-computer-gamesIn this talk Michael Sternberg of Imperial reports how their research on protein modelling has led to the development of computer games with a role in scientific education. At Imperial, Chris Reynolds has developed a web-based molecular graphics resource EzMol which is a simple-to-use display of protein structures. In collaboration with Frederic Fol Leymarie, William Latham and their team at Goldsmiths, we have developed the BioBlox suite of scientific-based computer games based around protein docking. BioBox3D is a serious crowd-sourced game for predicting protein/protein docking. BioBlox2D is a fun-to-play game with scientific content for phone/tablet inspired by the recognition between proteins and small molecules. Finally, BioBloxVR is a virtual reality environment for protein docking inspired by BioBlox3D. We are exploring the opportunities for EzMol and BioBlox as educational resources. The projects were supported by the BBSRC.
Created at: 3rd BiVi Annual Meeting (2017).Prof. Michael J E SternbergMolecular2017-05-15

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

ChIP-seq analysis using Rhttps://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Bori_Mifsud/README.mdhttps://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-5049bc9c-9bbb-4a6b-9244-37ed3980da0eChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis.Bori MifsudKathi ZarnackChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming